Plot Issues

1. Play out the sidequests anyway in the back burner

In a way this feels like a Shadowrun situation, and quite frankly if the players are chasing their own (maybe literal) ghosts, the factions are going to hire someone available to do it. Let the party handle their own stuff and a rival party gets the job. You can resolve the quest any way you feel appropriate for where the plot will develop, but now the players need to fight for their reputations. The next player plot hook could be buried in the rival groups.

2. Why not mix it up?

If the party is supposed to be a group of characters with high impact on their world, there is a way to make the character plots intercede with the core plots, even if they happen just a little off kilter from what you need to accomplish like the job is straightforward but Bob's old nemesis just can't see it go well, or George's scorned love demands a favor in exchange for forgiveness, or Nell's long lost sister might be in the mark faction's castle/town/whatever. While they may seem very divergent, the plot device has a setting for looping things together in the strangest of ways such that they all become related and keep the party together.

3. PC the NPC / NPC the PC

Do you have a specific way you want the quests to go? Follow one of the players on their sidequest (and anyone else with reason to be involved) and pre-gen NPCs for the rest of the characters to play - including a core enough personality to keep them involved. Meanwhile, the party does their quest. It might not be the smoothest accomplishment but it would then be up to you as the DM for embellishments but do reward the core party with the quest items for the players performing well in the side arc. This also gives you play room for fuzzy memory parts that you need to ad hoc or retcon.

4. Save this campaign for later

If the players are giving you enough plot to run a full game, it may mean that you should save this campaign for when you have a more attentive party - especially one where you can tell the players what they're in for to make characters in reaction to it. This is my least favorite idea but if they have these in depth characters that run parallel to the world you're running, it may be worth considering.

Motivation Issues

I'm hoping these are not the CN players who just enjoy what I call the Video Game Experience. To me, the Video Game Experience is that to the player, anything in the environment they can interact with needs to be important, monsters are just experience, and the plot itself doesn't necessarily need to matter if they get the levels and the loot. In this case they are almost turning themselves into NPCs if their actions really have nothing to do with the party.
It may be worthwhile to sit down with them to explain that these characters need a few tweaks to make the game harmonic. While a character can be selfish, the fact is that it's hard to run a full party with the truly self indulgent within it. Tell them that they can keep their characters, perhaps even as they are but the player becomes responsible at least up front with why the character is with the group. After encountering a situations where the characters don't mesh or the lone wolf amidst the team, DMs in my area have started telling people that even if they make characters on their own, it's up to them to make party cohesion work. Sometimes it doesn't matter and the DM holds the leash for some major plot hook, but the fact is that in the seemingly sandbox world you have, the party dynamic is player driven.

You could present the game in a more reactive fashion.

If the players do not appear to be making any kind of indications of the sort of actions that they would like to take then you could simply present low-importance information back to them and again prompt them for action.

For instance: The players would like a means of entering a city and have their reasons not to do so in conventional ways (through the front gate - through the guards).

You could start be describing the city as being... "...on a slope, with most battlements appearing to be well-maintained, the grey slate mostly devoid of growths and only the faint shadows of the sun high in the sky betraying the existence of minor weather erosion. The breeze blows warmly across the landscape and activity at the gate seems calm."

In the lack of an indication of action you could prompt the group with the soft suggestion - "Would you like to explore further?"

(Side Note - if the response is something as low-brow as "we wait a little to see what happens" then an appropriate response could be "You wait a few minutes and watch as a small flock of pigeons rise and fall in the distance over the rafters... Nothing of further note catches your attention. What would you like to do now?" This presents the low-importance information mentioned earlier - unless there is good reason to add information (a time-line like an approaching storm or a nearby threat))

If yes then "OK. Tell me who in the group is going to be exploring and in what manner. Are you looking for anything?"

And in response to the lackluster "Looking for a way in" - "OK - You need to tell me specifically what kind of way in you are looking for and how you are going to do it"

This will engage the players and certain avenues may present options to you. Perhaps scouting the walls in a careless or unstealthy manner might result in a challenge from atop one of the watch towers. Or perhaps they will happen upon a small group of shady characters with which interaction might occur.

You may also be presented with options that you had not considered.

A search of the walls for a means to scale it might reveal a particular location between battlements where external plumbing has been affixed externally to the wall, leading downwards and terminating a short way above a lonely sewage wagon. This would present the possibility of an easier climb DC should they choose this way to enter - although there is no guarantee that it will not be detected or that it will be safe. The small stream inlet further north around the city (assuming that the character searches further) might prove a better bet - especially if you can swim.

Although the players needn't be told that unless they test the waters first - that is part of the fun of being a GM - you don't need to worry about common sense on behalf of the players - you can provide warnings of difficulties if you wish.

In this way you are presenting the kinds of choices that the players elicit from you. If they don't appear remotely interested in going through the gate then there is no need to present the hint (if specifically searched for) that the guard might accept a payoff - or that disguises might work due to the apparent lazy disposition of the guards in general.

Of course you will occasionally want to prod the group if they end up in a situation with no clear way forward. If boredom is setting in and the group is stuck looking for posters of jobs at the guard house then perhaps their attention might be drawn to a short old man who watches them intently from outside the door. That may play out in various ways - whether to present a task or to present a new foe or to direct the players to a location that they would be more likely to find work.

Alternatively it is possible to draw upon the characters' background history - a little clue that occasionally pops up here and there. Whether it materializes as expected is not important - it helps to provide direction and direction is a precursor to momentum.

Presenting secondary events

When you spend time designing secondary plots for the party to stumble upon it is understandable that you would 'wish' for the party to stumble upon them even if they might not otherwise do so.

While you could certainly place all these encounters (conveniently) in the path of your players, there are several factors to consider:

• Conservation of effort and resources - Is it of particular importance for the players to encounter this sub-plot at this juncture of the adventure? You could perhaps look at different ways to capitalize upon the players missing this plot-line and any reasonable clues (such as the occasional unexplained whiff of rotten meat - or a suspiciously intact section of skeleton laying near a dump site in the sun (perhaps waiting for the dark to saunter its way toward an evil source)) that you might have placed in their path.

Would it be economical for this basement-dwelling dabbler necromancer to 'move' to a run-down shack in an unnaturally silent part of the forest (think 'Evil Dead')? Or perhaps a next town if the concept would work better in an urban environment.

One last possibility is introducing the possibility of consequences for events that are not encountered and tackled. Perhaps failing to notice the dabbler necromancer would result in an increased incidence of undead attacks in the surrounding country-side as his poorly contained energies seep away and awaken a worse evil than he or she could ever have imagined. This could also apply to the potion shop ruckus - a few ill-mixed ingested potions could release a crazily mutated humanoid upon a rampage.

• Suspiciously peaceful aftermath - If your players encounter nothing but resistance from varying seemingly unrelated forces before completing the main event, and emerge to sunshine and rainbows within a suddenly peaceful city then one or two players might begin to suspect that one or more secondary plots were contrived - placed before them - possibly denting the suspension of belief that goes with good role playing games (its not so likely if they actively pursued reasonably challenging and scarce clues). Even if you don't happen to have any good secondary plots left for this city you could always fall back on the consequences of the breakdown of the structure of order in part or all of the city (The guards are distracted. Looters ahoy!).

• Player conditioning towards proactive approach - If the players do not express any desire to explore the rest of the city then they do not have to. Once again you can recycle materials for other locations in terms of shop descriptions and the like (just be sure to keep track of what NPCs and places you put in which locations - jot notes on the fly). Furthermore you could occasionally tease the players by having a couple of travelling NPC casually comment between themselves that "The 20% sale was a novel idea", or that the "Artifact auction was popular" or that "Villagers have started disappearing in the night", etc.

Eventually the players may get the idea that it is worthwhile to get a small idea of a city as you never know what you might find.

Hint - If you are not into detailing maps then you could do worse than to set all the locations (or clusters of locations) on a probability chart. If they roll successfully for a particular location then you could describe that section in shallow detail similarly to when you described the city at first sight - let them explore and direct the flow. Rerolls can attempt to avoid areas already explored - alternatively a good streetwise test (even characters can get lost in some places that are big enough).

Conservation of energy as a GM

While some of these thoughts may hopefully prove useful to yourself in conducting your games, remember that they are a set of suggestions that need not be implemented in full. You will find it desirable to determine how deeply you wish to describe your world and an excess amount of it may be pleasing but it may also entail a greater degree of creative involvement on your part. This is why I mentioned certain time-saving elements like use of pre-determined probability charts - these are tools intended to take a little of the burden off your mind - but should not serve as an obstacle to your doing what you wish to do (you can fudge a roll or allow direct movement if it takes your fancy) - after all, the tools serve you, not vice-versa.